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Atomistic Toolkit MCP Server

@XirtamEsrevni

代码仓库

基本信息

分类

开发工具

许可证

MIT

传输方式

stdio

作者

XirtamEsrevni

关于 Atomistic Toolkit MCP Server

An MCP-compatible server providing atomistic simulation capabilities through ASE, pymatgen, etc.

#atomistic#simulation#mcp#ase#pymatgen

Atomistic Toolkit MCP Server 配置

使用下面的配置,将此服务器添加到你的 MCP 客户端。

{
  "mcpServers": {
    "mcp-atomictoolkit": {
      "command": "python",
      "args": [
        "main.py"
      ]
    }
  }
}

Atomistic Toolkit MCP Server 工具

工具列表暂未提供

当前收录暂时没有可展示的工具列表，不代表服务没有工具。请查阅项目文档了解支持的能力。

工具是从 README 中自动提取的。维护者可以在 ## Tools 标题下列出工具,即可填充这部分内容。

概览

What is Atomistic Toolkit MCP Server?

An MCP (Model Context Protocol) server for atomistic modeling workflows, powered by ASE, pymatgen, and modern machine‑learning interatomic potentials. It exposes ready‑to‑call tools for building structures, running geometry optimization and molecular dynamics, analyzing structures and trajectories, and providing downloadable file artifacts.

How to use Atomistic Toolkit MCP Server?

Requires Python 3.11+. Install dependencies with pip install -r requirements.txt, then start the HTTP server with uvicorn mcp_atomictoolkit.http_app:app --host 0.0.0.0 --port 10000 (or python main.py). For desktop MCP clients, use STDIO mode: python -m mcp_atomictoolkit.mcp_server. Verify with curl -s http://localhost:10000/healthz.

Key features of Atomistic Toolkit MCP Server

  • MCP‑native workflows via FastMCP tools
  • Structure generation: bulk, surface, molecule, supercell, amorphous, liquid, bicrystal, polycrystal
  • Optimization with MLIPs (kim default, nequip, orb)
  • Molecular dynamics (Velocity Verlet, Langevin, NVT Berendsen)
  • Analysis: RDF, MSD, VACF (Green‑Kubo), thermodynamic trends
  • Downloadable artifacts (xyz, extxyz, cif, traj, png, svg, csv, dat)

Use cases of Atomistic Toolkit MCP Server

  • Automate atomistic simulation workflows without hand‑writing scripts
  • Run structure building, optimization, and MD from LLM‑based agents or desktop clients
  • Analyze trajectories for diffusion coefficients and correlation functions
  • Generate and share simulation artifacts (files + plots) via download URLs

常见问题

1

What modes does the server support?

It supports both Streamable HTTP (via uvicorn) and STDIO (for desktop MCP clients). STDIO mode must keep stdout clean of print/logging.

2

What file formats are available for download?

Artifacts can be downloaded in `.xyz`, `.extxyz`, `.cif`, `.traj`, `.png`, `.svg`, `.csv`, `.dat`, and more.

3

What endpoints does the server expose?

Primary MCP endpoint is `POST /`. Also includes `GET /healthz`, `GET /docs`, `GET /.well-known/mcp/server-card.json`, `GET /artifacts/{artifact_id}/{filename}`, and `/sse/`.

4

Can I deploy the server in a container or on Render?

Yes. A `render.yaml` and a `Dockerfile` are provided. Default Docker command runs on port 7860.

5

What optimization and MD parameters can be tuned?

Optimization supports `max_steps`, `fmax`, `maxstep`, `alpha`, and constraints (fixed atoms, bonds, cell). MD supports `temperature_K`, `friction`, `taut`, and multiple integrators (NVE, NVT‑Langevin, NVT‑Berendsen).

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